Originally, a kneecap. The phrase "bust a cap" originated in Northern Ireland several years before entering urban gangsta culture, and referred to the nonlethal (but fantastically painful and disabling) practice of firing a firearm at close range into the crook of the knee. The practice served, and in some areas continues to serve, primarily as an intimidation tactic, and the victim becomes a hobbling reminder of what happens to "the enemy."

I told him I'd bust a cap in his ass, but it turns out he didn't have an asscap after all, so I let him go.